snakemake.pe_analysis
¶
Module Contents¶
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snakemake.pe_analysis.
pe_combine_param_best_fits_stats
(plots_dir, fileout_param_estim_best_fits_details)¶ Combine the statistics for the parameter estimation details
Parameters: - plots_dir – the directory to save the generated plots
- fileout_param_estim_best_fits_details – the name of the file containing the detailed statistics for the estimated parameters
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snakemake.pe_analysis.
pe_combine_param_ple_stats
(plots_dir, fileout_param_estim_details)¶ Combine the statistics for the parameter estimation details
Parameters: - plots_dir – the directory to save the generated plots
- fileout_param_estim_details – the name of the file containing the detailed statistics for the estimated parameters
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snakemake.pe_analysis.
pe_ds_preproc
(filename, param_names, logspace=True, all_fits=False, data_point_num=0, fileout_param_estim_summary="param_estim_summary.csv")¶ Parameter estimation pre-processing. It renames the data set columns, and applies a log10 transformation if logspace is TRUE. If all.fits is true, it also computes the confidence levels.
Parameters: - filename – the dataset filename containing the fits sequence
- param_names – the list of estimated parameter names
- logspace – true if the data set shoud be log10-transformed.
- all_fits – true if filename contains all fits, false otherwise
- data_point_num – the number of data points used for parameterise the model. Ignored if all.fits is false
- fileout_param_estim_summary – the name of the file containing the summary for the parameter estimation. Ignored if all.fits is false
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snakemake.pe_analysis.
pe_objval_vs_iters_analysis
(model_name, filename, plots_dir)¶ Analysis of the Objective values vs Iterations.
Parameters: - model_name – the model name without extension
- filename – the filename containing the fits sequence
- plots_dir – the directory for storing the plots
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snakemake.pe_analysis.
pe_parameter_density_analysis
(model_name, filename, parameter, plots_dir, thres="BestFits", best_fits_percent=100, fileout_param_estim_summary="", logspace=True, scientific_notation=True)¶ Parameter density analysis.
Parameters: - model_name – the model name without extension
- filename – the filename containing the fits sequence
- parameter – the name of the parameter to plot the density
- plots_dir – the directory for storing the plots
- thres – the threshold used to filter the dataset. Values: “BestFits”, “CL66”, “CL95”, “CL99”, “All”.
- best_fits_percent – the percent of best fits to analyse. Only used if thres=”BestFits”.
- fileout_param_estim_summary – the name of the file containing the summary for the parameter estimation. Only used if thres!=”BestFits”.
- logspace – true if the parameters should be plotted in logspace
- scientific_notation – true if the axis labels should be plotted in scientific notation
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snakemake.pe_analysis.
pe_parameter_pca_analysis
(model_name, filename, plots_dir, best_fits_percent=100)¶ PCA for the best fits of the estimated parameters.
Parameters: - model_name – the model name without extension
- filename – the filename containing the fits sequence
- plots_dir – the directory for storing the plots
- best_fits_percent – the percent of best fits to analyse. Only used if thres=”BestFits”.
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snakemake.pe_analysis.
pe_sampled_2d_ple_analysis
(model_name, filename, parameter1, parameter2, plots_dir, thres="BestFits", best_fits_percent=100, fileout_param_estim_summary="", logspace=True, scientific_notation=True)¶ 2D profile likelihood estimation analysis.
Parameters: - model_name – the model name without extension
- filename – the filename containing the fits sequence
- parameter1 – the name of the first parameter
- parameter2 – the name of the second parameter
- plots_dir – the directory for storing the plots
- thres – the threshold used to filter the dataset. Values: “BestFits”, “CL66”, “CL95”, “CL99”, “All”.
- best_fits_percent – the percent of best fits to analyse. Only used if thres=”BestFits”.
- fileout_param_estim_summary – the name of the file containing the summary for the parameter estimation. Only used if thres!=”BestFits”.
- logspace – true if the parameters should be plotted in logspace
- scientific_notation – true if the axis labels should be plotted in scientific notation
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snakemake.pe_analysis.
pe_sampled_ple_analysis
(model_name, filename, parameter, plots_dir, fileout_param_estim_summary, logspace=True, scientific_notation=True)¶ Run the profile likelihood estimation analysis.
Parameters: - model_name – the model name without extension
- filename – the filename containing the fits sequence
- parameter – the parameter to compute the PLE analysis
- plots_dir – the directory to save the generated plots
- fileout_param_estim_summary – the name of the file containing the summary for the parameter estimation
- logspace – true if parameters should be plotted in logspace
- scientific_notation – true if the axis labels should be plotted in scientific notation